[gmx-users] N-glycosylation of a protein

Steffen Wolf swolf at bph.rub.de
Tue Jul 24 16:28:43 CEST 2007

Hi Eric,
one way to fix the problem is to define a residue in the force field
.rtp file for a "new" amino acid consisting of Asn + the hydrocarbon.
That way GROMACS can create the topology of the holoprotein while
running pdb2gmx over it.
Hope that helps
> Hi,
> I try to start a simulation with a N-glycosylated protein. I used
> glyprot to attach the sugar chains to the asn residues. But then.. I
> create a topology for the sugars, then merge it with the toplogy of
> the protein? What about the linkage between the protein and the sugar?
> Thanks,
> Eric
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Dipl.-Chem. Steffen Wolf
Fellow of the Ruhr-University Research School
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: swolf at bph.rub.de
Web: http://www.bph.rub.de 

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